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biopet.biopet
Commits
1c155c9b
Commit
1c155c9b
authored
Sep 09, 2015
by
Peter van 't Hof
Browse files
Change vars to vals, possible because method 'addTagresultToTaglib' is now changed
parent
9b465609
Changes
2
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
View file @
1c155c9b
...
...
@@ -88,8 +88,7 @@ object SageCreateLibrary extends ToolCommand {
}
}
var
tagRegex
:
Regex
=
null
var
geneRegex
=
"""ENSG[0-9]{11}"""
.
r
val
geneRegex
=
"""ENSG[0-9]{11}"""
.
r
val
tagGenesMap
:
mutable.Map
[
String
,
TagGenes
]
=
mutable
.
Map
()
...
...
@@ -114,7 +113,7 @@ object SageCreateLibrary extends ToolCommand {
if
(!
commandArgs
.
input
.
exists
)
throw
new
IllegalStateException
(
"Input file not found, file: "
+
commandArgs
.
input
)
tagRegex
=
(
commandArgs
.
tag
+
"[CATG]{"
+
commandArgs
.
length
+
"}"
).
r
val
tagRegex
=
(
commandArgs
.
tag
+
"[CATG]{"
+
commandArgs
.
length
+
"}"
).
r
var
count
=
0
logger
.
info
(
"Reading fasta file"
)
...
...
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
View file @
1c155c9b
...
...
@@ -85,7 +85,7 @@ class SageCreateLibaryTest extends TestNGSuite with MockitoSugar with Matchers {
val
reader
=
FastaReaderHelper
.
readFastaDNASequence
(
new
File
(
input
))
val
records
=
reader
.
iterator
.
toList
tagRegex
=
(
"CATG"
+
"[CATG]{"
+
17
+
"}"
).
r
val
tagRegex
=
(
"CATG"
+
"[CATG]{"
+
17
+
"}"
).
r
val
record1
=
records
(
0
)
val
record2
=
records
(
1
)
...
...
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